Best Probiotics for Gluten Intolerance: A Comprehensive Guide

best probiotics for gluten intolerance

Probiotics are well known for their potential to promote overall health and support a healthy digestive system. As a result, the use of probiotics has skyrocketed in recent years. But if, like me, you live with non celiac gluten sensitivity, your choices may be more limited. Join me as I explore the health benefits of probiotics and discover the best probiotics for gluten intolerance. I’ll also look at things to consider when choosing a probiotic supplement.

The information provided is for general informational and educational purposes only. It is not intended as medical advice, and it should not be used to diagnose or treat any health condition or illness. Always seek the advice of a qualified healthcare provider with any questions you may have regarding a medical condition or your individual health.

Personal experience with probiotics

Throughout the years I’ve had various healthcare providers recommend probiotics for me and my family.

Once my daughter had a stomach bug that left her with painful cramps and diarrhea. Her initial symptoms subsided within a few days. But over the next month her symptoms returned every weekend. I’ve never seen my daughter in so much pain. 

A gastroenterologist recommended probiotics. He said sometimes stomach bugs cause the gut flora to get thrown out of whack. Foods normally tolerated can cause a reaction as a result. In her case it was beef. 

My daughter needed a reboot. She began taking probiotics. Within a few weeks, her symptoms completely subsided.

Once, I began taking probiotics to  treat constipation. Initially it worked well. I mean very, very well. But after a few days, it stopped working altogether. 

Years later I tried probiotic supplements again. This time, I developed dermatographia after a few days. This is a skin condition where the skin develops raised welts when scratched. 

This wasn’t my first rodeo with the skin condition. For me, it’s usually a sign that something I’ve ingested or used on my skin doesn’t agree with me.

I should mention that I’m very, very sensitive. I have several food allergies and sensitivities and I never know what I will react to. Especially since developing pemphigus vulgaris, an autoimmune disease.

I even reacted to gluten-free, dairy-free yogurt. What gives?

I began to think probiotics just weren’t in the cards for me. Maybe you can relate. I’ll talk about allergies and sensitivities a little later, so stay tuned. 

What are probiotics

Probiotics are live microorganisms found in fermented foods and supplements. Referred to as “good bacteria” or “beneficial bacteria”, these microorganisms interact with immune cells in our gastrointestinal tract. This helps to promote a healthy immune system, one that neither overreacts or under reacts to threats. 

When consumed in adequate amounts, probiotics assist in maintaining overall health, disease prevention, and treatment of various health conditions.

Many of the friendly bacteria found in probiotics are commonly found in our gut microbiome. They effectively crowd out populations of bad bacteria. In addition, good bacteria produce acids that prevent bad bacteria from growing unchecked.  

This reduces the risk of gastrointestinal infections and promotes an optimal environment for digestion. 

But the story doesn’t end there. In addition to gut and immune health,  probiotic supplements are also promoted for vaginal health and even brain health.

What is the meaning of gluten intolerance

Gluten proteins are found in wheat, barley and rye. For individuals with a gluten intolerance, also known as non-celiac gluten sensitivity,  ingesting gluten is problematic. 

Symptoms can range from abdominal discomfort, bloating, constipation, diarrhea, and fatigue to brain fog, anxiety headaches and rash. They may last several hours or even days after consuming gluten.

Gluten intolerance isn’t the same thing as celiac disease.

Like gluten intolerance, celiac disease patients react to gluten when consumed. In fact, symptoms are very similar. Additional symptoms include, bulky, bad-smelling bowel movements, pain in the joints, bones and abdomen, depression and anxiety.

Celiac disease is an autoimmune disorder which can ultimately damage the small intestine. 

In sensitive people, even trace amounts of gluten can cause a bad reaction. Switching  to a gluten-free diet is the best approach for managing either gluten intolerance or celiac disease. 

While this may be challenging at first, success is possible. Whether eating out or preparing your own gluten-free foods, these 10 Gluten-Free Lifestyle Hacks will give you the headstart you need.

What are probiotic strains and why do they matter

Scan any aisle stocked with probiotic supplements and you’re sure to see labels that refer to probiotic strains that are “diverse” or “specially selected.” 

A probiotic strain refers to  a specific microorganism. Different probiotics contain different strains, each with different characteristics. These characteristics make them suitable for treating various health conditions. There are over 500 probiotic strains.

Probiotic strains can be further classified by genus, which represent closely related species. For example Streptococcus thermophilus and Streptococcus salivarius belong to the Streptococcus genus.

Bifidobacterium bifidum and  Bifidobacterium breve belong to the Bifidobacterium species.

What is CFU in probiotics

Colony Forming Units or CFU refers to the number of live and active microorganisms in probiotic foods  or supplements. This includes beneficial bacteria and yeast. 

While higher counts don’t always equate to superiority, CFU count is an important consideration when shopping for a probiotic product, as it is an indication of the probiotic’s potency.

It’s not uncommon to see CFU counts in the millions and even billions. The latter may be better suited for people treating specific medical conditions.

What are the health benefits of probiotics

Probiotics help improve gut health
Probiotics help improve gut health

Probiotics are primarily classified into 2 groups: lactic acid bacteria and yeast.  Each has different health benefits.

Benefits of lactic acid bacteria

Lactic acid bacteria is a food grade bacteria used in the fermentation process. Food manufacturers use lactic acid bacteria to improve the flavor and texture of food. 

There are many health benefits of consuming foods with lactic acid bacteria including:

  • Improved digestion.
  • Enhanced ability to absorb nutrients.
  • Enhanced ability to produce beneficial compounds like B vitamins and fatty acids. 
  • Increased protection that helps our  immune system to protect us from infections and illnesses.
  • Regular bowel movements.
  • Certain strains help with the digestion of lactose, a milk sugar associated with lactose intolerance.
  • Weight loss  and obesity prevention.
  • Some strains contribute to healthy vaginal microbiota by balancing out PH levels. 

There are hundreds of strains of lactic acid bacteria that are commercially used. New strains are continually being discovered. 

Probiotic yeast was originally isolated from the skin of 2 tropical fruits, lychee and mangosteen. This yeast is non-pathogenic  and is used for its probiotic properties. Saccharomyces boulardii is the most commonly used probiotic yeast. 

Health benefits of probiotic yeast include:

  • Supports gastrointestinal health by maintaining a healthy balance of microorganisms in the gut.
  • Beneficial for managing diarrhea associated with antibiotic use, traveler’s diarrhea and pathogens like C-difficile.
  • Effective at relieving symptoms of Irritable Bowel Syndrome (IBS) including bloating and abdominal discomfort.
  • Helpful in treating  symptoms of Irritable Bowel Diseases like Crohn’s disease and ulcerative colitis.
  • Helps prevent infections of the gut by crowding out harmful pathogens.
  • Assists with breaking down lactose, a milk sugar.

Probiotics for vaginal health

You may have heard that eating yogurt while taking antibiotics can help prevent yeast infections in women, but have you ever wondered why? 

A healthy vaginal microbiome has dominating levels of Lactobacillus, a good bacteria. Antibiotics kill good bacteria along with the bad bacteria when fighting infections. Yogurt rich in lactobacillus acidophilus is effective for restoring healthy levels. 

You may already be quite  familiar with lactobacillus acidophilus. It’s name is commonplace. But  other bacterial strains, particularly in the Lactobacillus species, also effectively treat candida and bacterial vaginosis. This includes Lactobacillus rhamnosus and Lactobacillus reuteri to name a few.

Probiotics for gut health

A healthy gut microbiome has a diverse population of good bacteria. These bacteria fight harmful pathogens, restore healthy bowel movements, and improve digestion.

For abdominal pain caused due to irritable bowel syndrome (IBS), probiotics may help.  Not only do probiotics reduce discomfort and bloating,  but they also help reduce inflammation.

Bifidobacterium lactis, lactobacillus plantarum and saccharomyces boulardii  have shown promise in treating IBS and leaky gut syndrome

The latter is a  condition that causes proteins and undigested food particles to pass through the intestinal lining. Eventually these particles wind up in the bloodstream and have been linked with food allergies, asthma, headaches and more. 

Bifidobacterium lactis improves overall gut health by assisting with digestion. It also helps to regulate bowel movements and relieves the cramping, bloating and abdominal distension of  irritable bowel syndrome (IBS). 

Probiotic for immune health

Seventy percent of the immune system lives in the gut. So the fact that probiotics help to maintain a healthy gut microbiome directly impacts the immune system. 

For people with autoimmune disease, B. bifidum, Ruminococcus obeum, Blautia coccoides, and L. casei have have been known to regulate the inflammatory response in several studies.  

But as previously mentioned, some autoimmune conditions may be adversely affected by probiotic supplements, so always consult with your physician. 

Results may vary from person to person.

Probiotics for brain health

Research has exposed the connection between the brain and the gut. This is referred to as the gut-brain axis. In fact, bidirectional communication occurs between the gut and the brain.  A balanced gut microbiome can send signals to the brain that may impact mood, behavior and cognitive function. 

Furthermore, Lactobacillus and Bifidobacterium are known to produce neurotransmitters like serotonin and dopamine that impact bidirectional communication

Best probiotics for gluten intolerance

Celiac disease is a chronic autoimmune disorder triggered by the consumption of gluten. 

For people with celiac disease and non-celiac gluten sensitivity probiotics may help manage stubborn symptoms that remain even after avoiding gluten. These may include bloating, gas, constipation and diarrhea.

In many instances, other underlying conditions exist like FODMAP intolerance, lactose intolerance, SIBO, histamine intolerance, and IBS.  

Strains in the Lactobacillus and Bifidobacterium species, as well as Saccharomyces boulardii, a yeast, may be beneficial.  

There’s still lots to uncover about how probiotics can help people with celiac disease. 

It’s important to remember, there’s no cure for celiac disease or gluten intolerance due to non-celiac gluten sensitivity. Strict avoidance of gluten is the only real solution.

Who shouldn’t take probiotics

People with a compromised  immune system should avoid taking probiotic supplements. This includes people who have had organ transplants or are undergoing chemotherapy. This is because probiotics contain live bacteria, and in some cases, yeast.

Live microorganisms can pose a risk of infection for people with severely compromised immune systems.

People with certain autoimmune conditions may also want to avoid taking probiotic supplements. If you’re uncertain, check with your healthcare provider. 

Can you be allergic to probiotics

Probiotic supplements can cause itchiness and even skin rashes, but this is rare. Also, keep in mind this can have a number of causes. You may just be allergic to another ingredient in the supplement. 

Remember I mentioned I couldn’t even tolerate yogurt? Well it turns out I was sensitive to another ingredient in the yogurt…carrageenan. This ingredient is sourced from red seaweed and is used as a thickener and emulsifier. There’s been controversy around this ingredient in recent years. Some believe it causes inflammation and can also cause damage to the digestive system.

I found out I was allergic to carrageenan by trial and error. I began experimenting with several gluten-free, dairy-free yogurts that didn’t contain it. Some were coconut-based, others were soy-based. All are vanilla flavored because I react to several fruits.

In any event, if you’re gluten intolerant, proceed with caution. Not all probiotic supplements labeled gluten-free are totally free of gluten. Supplements are not regulated by the FDA.

One study found small traces of gluten in probiotic supplements labeled gluten-free.

For one thing, never assume a probiotic supplement is gluten-free. Always look for the gluten-free label. If you’re extra sensitive to gluten, make sure the supplement is certified by a 3rd party.

For this reason, I love, love, love Garden of Life Probiotics, Once Daily Women’s. It’s gluten-free certified meaning it’s gone through stringent testing by a 3rd party.

If you have a reaction to any probiotic, consider changing brands or even trying different probiotic strains. But first, consult with your healthcare provider.

You May Also Want To Read

How to Manage Your Autoimmune Disease With Dietary Changes

Gut Health and the Immune System: What You Need to Know

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Low-FODMAP Diet Provides Proven Results For Multiple Chronic Conditions

Free Constipation Printable List of High Fiber Foods

How to Beat Constipation Naturally: 6 Tips That Don’t Involve Laxatives

What are the main sources of probiotics

Probiotics can be found in a variety of sources. The main sources of probiotics are yogurt, fermented foods like sauerkraut, kimchi, and miso, and probiotic supplements. Live cultures of probiotic bacteria can also be found in drinks like kefir, kombucha and fermented fruit juices.

Gluten-free probiotic foods

Gluten-free yogurt
Gluten-free yogurt is a good source of probiotics

Yogurt is just cultured milk so it’s naturally gluten-free. However, some yogurts contain added flavors and additives which may contain gluten. It’s also possible for cross-contamination to occur during manufacturing.  

Not all yogurts contain probiotics. Make sure yogurt labels say “live and active cultures” or “contains probiotics”. 

Gluten-free probiotic yogurt: 

  • Chobani
  • Yoplait Original
  • Dannon Light and Fit Greek Yogurt
  • Siggi’s Yogurt
  • Silk Dairy-Free Yogurt Alternative
  • Cocojune (also dairy-free)

Sauerkraut is a rich source of probiotics. Made from  fermented cabbage that has been finely shredded, sauerkraut is naturally gluten-free. 

Sauerkraut contains several species including Leuconostoc mesenteroides, Lactobacillus plantarum, Lactobacillus brevis, Pediococcus, and Enterococccus. Avoid pasteurized brands as the pasteurization process kills active bacteria. 

Sauerkraut is naturally gluten-free, with many brands only containing fermented cabbage, salt and water. But not all brands are probiotics so be sure to read the label.

Gluten-free sauerkraut brands: 

Kimchi is a Korean dish that combines fermented and salted vegetables, particularly napa cabbage and Korean radishes,  with a variety of spices. Some spices you can expect to find are fish sauce, red pepper flakes, scallions and red chili pepper. Like sauerkraut, kimchi is rich in Lactobacillus.

Gluten-free kimchi brands:

Miso is a paste made from fermented soybeans. It usually consists of water, salt, soybeans, and koju. Koju is made from fermented rice, barley or other grains. Miso is naturally gluten-free, providing none of its ingredients, such as the koju, contain gluten. For example, barley is not gluten-free.

Miso is often used in stir-fry, sauces and soups, as well as salad dressing, and as an alternative to soy sauce. But here’s the catch…high temperatures can kill the probiotic strains. It’s best to either use miso in cold or add miso to dishes once the pot has cooled to below 70C/158F.

Gluten-free miso brands:

Other probiotic foods

Other gluten-free probiotic foods include tempeh, pickles, fermented cheeses, traditional buttermilk and natto. 

Gluten-free probiotic drinks

Gluten-free kefir
Gluten-free kefir contains multiple probiotic strains

Kefir is made from cultured milk just like yogurt. However, the texture of kefir is thinner than yogurt. And Kefir contains a larger variety of probiotic strains than yogurt…12 on average. While 

yogurt contains about 50 million CFUs of probiotics, kefir contains up to 10 billion CFUs. Water kefir, a dairy-free beverage, is also available.

Gluten-free kefir brands:

  • Lifeway Organic Whole Milk Kefir 
  • Green Valley Organic Kefir
  • Maple Hill Organic Kefir

Kombucha is an effervescent drink with a tangy, mildly sweet flavor. It’s made from fermented tea, sugar, cultured bacteria and yeast. It can be flavored with fruits, herbs and even spices.

As a probiotic, kombucha is known to help promote a healthy gut. However, people with IBS should limit their intake as it’s high in FODMAPS (fermentable oligosaccharides, disaccharides, monosaccharides and polyols).

Gluten-free kombucha brands

  • Remedy Kombucha Tea Organic Drink – Sugar Free, Keto, Vegan & Gluten Free
  • Health-Ade Canned Kombucha Tea Organic Drink, Non-GMO, Vegan, Gluten Free
  • Humm Probiotic Kombucha Zero Sugar Variety Pack – No Refrigeration Needed, Keto Friendly, Organic, Vegan, Gluten Free

Best gluten-free probiotic supplements

probiotic supplements
Probiotic supplements

Probiotic supplements enable you to target specific probiotic strains. This is helpful when you want to treat a particular medical condition. 

Some things to consider when purchasing probiotic dietary supplements include:

  • Ingredients – Examine carefully to be certain they don’t contain anything you’re allergic or sensitive to.
  • Probiotic strains and CFU count – consult with your healthcare provider to determine levels that are appropriate for your health goals and medical conditions.
  • Expiration date – the effectiveness of probiotics begins to diminish after the expiration date.
  • Third-party certification ensures that the label on the probiotics is accurate.

Gluten-free probiotic supplements

In addition to being gluten-free, the brands below contain a diverse population of probiotic strains. They are also free of dairy and other allergens. 

  • Garden of Life Once Daily WomenHighlights: Certified gluten free, 50 billion CFU, 16 probiotic strains – gluten-free, dairy-free, soy-free.
  • Stonehenge Health ProbioticsHighlights: 55 billion CFU, 16 probiotic strains, prebiotic, GMP certified, delayed release – gluten-free, dairy-free, soy-free, vegetarian, peanut-free, dairy-free, no preservatives
  • Renew Life – Women’s Care ProbioticHighlights: 25 billion CFU, 12 probiotic strains – gluten-free, dairy-free, soy-free
  • New Rhythm ProbioticsHighlights: 50 billion CFU, 20 probiotic strains, 3rd Party Certified for Purity and Potency – gluten free and verified Free of Sugar, Soy, Yeast, Egg, Wheat, Corn, Peanuts, Fish, Shellfish, Magnesium Stearate, Artificial Ingredients, Fillers, Binders, Preservatives.


When it comes to promoting overall health, probiotics are a powerful ally.  From promoting digestive health and reducing gastrointestinal symptoms to supporting vaginal, immune and brain health, its benefits cannot be overstated. Consult with your healthcare provider to see if incorporating probiotic-rich foods or supplements is right for you.